samples/alkane/alkanes.md

#ifndef __ALKANES_MD__
#define __ALKANES_MD__

molecule{
  name = "methane";
  
  atom[0]{
    type="CH4";
    position( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "ethane";
  
  atom[0]{
    type = "CH3";
    position( 0.0, 0.0, 0.0 );
  }
  atom[1]{
    type = "CH3";
    position( 0.0, 1.54, 0.0 );
  }

  
  bond{
    members( 0, 1 );
  }
}

molecule{
  name = "ethane2";
  
  atom[0]{
    type = "CH3";
    position( 0.0, 0.0, 0.0 );
  }
  atom[1]{
    type = "CH3";
    position( 0.0, 1.54, 0.0 );
  }

  
  bond{
    members( 0, 1 );
  }
}


molecule{

  name = "propane";
  
  
  atom[0]{
    type = "CH3";
    position( -0.626, 1.407, 0.0 );
  }

  atom[1]{
    type = "CH2";
    position( 0.0, 0.0, 0.0 );
  }

  atom[2]{
    type = "CH3";
    position( 1.54, 0.0, 0.0 );
  }

  
  bond{
    members( 0, 1 );
  }

  bond{
    members( 1, 2 );
  }

  
  bend{
    members( 0, 1, 2 );
  }
}

molecule{

  name = "butane";
  
  
  atom[0]{
    type = "CH3";
    position( -0.626, 1.407, 0.0 );
  }

  atom[1]{
    type = "CH2";
    position( 0.0, 0.0, 0.0 );
  }

  atom[2]{
    type = "CH2";
    position( 1.54, 0.0, 0.0 );
  }

  atom[3]{
    type = "CH3";
    position( 2.166, -1.407, 0.0 );
  }
  

  bond{
    members( 0, 1 );
  }

  bond{
    members( 1, 2 );
  }

  bond{
    members( 2, 3 );
  }

  
  bend{
    members( 0, 1, 2 );
  }

  bend{
    members( 1, 2, 3 );
  }

  
  torsion{
    members( 0, 1, 2, 3 );
  }
}

molecule{

  name = "pentane";
  
  
  atom[0]{
    type = "CH3";
    position( -0.626, 1.407, 0.0 );
  }

  atom[1]{
    type = "CH2";
    position( 0.0, 0.0, 0.0 );
  }

  atom[2]{
    type = "CH2";
    position( 1.54, 0.0, 0.0 );
  }

  atom[3]{
    type = "CH2";
    position( 2.166, -1.407, 0.0 );
  }

  atom[4]{
    type = "CH3";
    position( 3.706, -1.407, 0.0 );
  }
  

  bond{
    members( 0, 1 );
  }

  bond{
    members( 1, 2 );
  }

  bond{
    members( 2, 3 );
  }

  bond{
    members( 3, 4 );
  }

  
  bend{
    members( 0, 1, 2 );
  }

  bend{
    members( 1, 2, 3 );
  }

  bend{
    members( 2, 3, 4 );
  }

  
  torsion{
    members( 0, 1, 2, 3 );
  }

  torsion{
    members( 1, 2, 3, 4 );
  }
}

molecule{

  name = "pseudoButane";
  
  
  atom[0]{
    type = "CH3";
    position( -0.626, 1.407, 0.0 );
  }

  atom[1]{
    type = "CH2";
    position( 0.0, 0.0, 0.0 );
  }

  atom[2]{
    type = "CH2";
    position( 1.54, 0.0, 0.0 );
  }

  atom[3]{
    type = "CH3";
    position( 2.166, -1.407, 0.0 );
  }
  

  bond{
    members( 0, 1 );
  }

  bond{
    members( 1, 2 );
  }

  bond{
    members( 2, 3 );
  }

  
  bend{
    members( 0, 1, 2 );
  }

  bend{
    members( 1, 2, 3 );
  }

  
  torsion{
    members( 0, 1, 2, 3 );
  }

  
  rigidBody[0]{
    
    members(0);
  }
  rigidBody[1]{
    
    members(1);
  }

  rigidBody[2]{
    
    members(2);
  }

  rigidBody[3]{
    
    members(3);
  }


}
#endif
Revision:	2489
Committed:	Tue Dec 6 16:49:59 2005 UTC (18 years, 7 months ago) by tim
File size:	2894 byte(s)
Log Message:	remove deprecated keywords from samples
#	Content
1	#ifndef __ALKANES_MD__
2	#define __ALKANES_MD__
3
4	molecule{
5	name = "methane";
6
7	atom[0]{
8	type="CH4";
9	position( 0.0, 0.0, 0.0 );
10	}
11	}
12
13	molecule{
14	name = "ethane";
15
16	atom[0]{
17	type = "CH3";
18	position( 0.0, 0.0, 0.0 );
19	}
20	atom[1]{
21	type = "CH3";
22	position( 0.0, 1.54, 0.0 );
23	}
24
25
26	bond{
27	members( 0, 1 );
28	}
29	}
30
31	molecule{
32	name = "ethane2";
33
34	atom[0]{
35	type = "CH3";
36	position( 0.0, 0.0, 0.0 );
37	}
38	atom[1]{
39	type = "CH3";
40	position( 0.0, 1.54, 0.0 );
41	}
42
43
44	bond{
45	members( 0, 1 );
46	}
47	}
48
49
50
51	molecule{
52
53	name = "propane";
54
55
56	atom[0]{
57	type = "CH3";
58	position( -0.626, 1.407, 0.0 );
59	}
60
61	atom[1]{
62	type = "CH2";
63	position( 0.0, 0.0, 0.0 );
64	}
65
66	atom[2]{
67	type = "CH3";
68	position( 1.54, 0.0, 0.0 );
69	}
70
71
72
73	bond{
74	members( 0, 1 );
75	}
76
77	bond{
78	members( 1, 2 );
79	}
80
81
82	bend{
83	members( 0, 1, 2 );
84	}
85	}
86
87	molecule{
88
89	name = "butane";
90
91
92	atom[0]{
93	type = "CH3";
94	position( -0.626, 1.407, 0.0 );
95	}
96
97	atom[1]{
98	type = "CH2";
99	position( 0.0, 0.0, 0.0 );
100	}
101
102	atom[2]{
103	type = "CH2";
104	position( 1.54, 0.0, 0.0 );
105	}
106
107	atom[3]{
108	type = "CH3";
109	position( 2.166, -1.407, 0.0 );
110	}
111
112
113
114
115	bond{
116	members( 0, 1 );
117	}
118
119	bond{
120	members( 1, 2 );
121	}
122
123	bond{
124	members( 2, 3 );
125	}
126
127
128	bend{
129	members( 0, 1, 2 );
130	}
131
132	bend{
133	members( 1, 2, 3 );
134	}
135
136
137	torsion{
138	members( 0, 1, 2, 3 );
139	}
140	}
141
142	molecule{
143
144	name = "pentane";
145
146
147	atom[0]{
148	type = "CH3";
149	position( -0.626, 1.407, 0.0 );
150	}
151
152	atom[1]{
153	type = "CH2";
154	position( 0.0, 0.0, 0.0 );
155	}
156
157	atom[2]{
158	type = "CH2";
159	position( 1.54, 0.0, 0.0 );
160	}
161
162	atom[3]{
163	type = "CH2";
164	position( 2.166, -1.407, 0.0 );
165	}
166
167	atom[4]{
168	type = "CH3";
169	position( 3.706, -1.407, 0.0 );
170	}
171
172
173
174
175	bond{
176	members( 0, 1 );
177	}
178
179	bond{
180	members( 1, 2 );
181	}
182
183	bond{
184	members( 2, 3 );
185	}
186
187	bond{
188	members( 3, 4 );
189	}
190
191
192	bend{
193	members( 0, 1, 2 );
194	}
195
196	bend{
197	members( 1, 2, 3 );
198	}
199
200	bend{
201	members( 2, 3, 4 );
202	}
203
204
205	torsion{
206	members( 0, 1, 2, 3 );
207	}
208
209	torsion{
210	members( 1, 2, 3, 4 );
211	}
212	}
213
214	molecule{
215
216	name = "pseudoButane";
217
218
219	atom[0]{
220	type = "CH3";
221	position( -0.626, 1.407, 0.0 );
222	}
223
224	atom[1]{
225	type = "CH2";
226	position( 0.0, 0.0, 0.0 );
227	}
228
229	atom[2]{
230	type = "CH2";
231	position( 1.54, 0.0, 0.0 );
232	}
233
234	atom[3]{
235	type = "CH3";
236	position( 2.166, -1.407, 0.0 );
237	}
238
239
240
241
242	bond{
243	members( 0, 1 );
244	}
245
246	bond{
247	members( 1, 2 );
248	}
249
250	bond{
251	members( 2, 3 );
252	}
253
254
255	bend{
256	members( 0, 1, 2 );
257	}
258
259	bend{
260	members( 1, 2, 3 );
261	}
262
263
264	torsion{
265	members( 0, 1, 2, 3 );
266	}
267
268
269	rigidBody[0]{
270
271	members(0);
272	}
273	rigidBody[1]{
274
275	members(1);
276	}
277
278	rigidBody[2]{
279
280	members(2);
281	}
282
283	rigidBody[3]{
284
285	members(3);
286	}
287
288
289	}
290	#endif